The ETE tutorial — ETE Toolkit - analysis and visualization of trees

ETE Toolkit 3.0 Changelog history The ETE tutorial Working With Tree Data Structures The Programmable Tree Drawing Engine Phylogenetic Trees Clustering Trees Phylogenetic XML standards Interactive web tree visualization Testing Evolutionary Hypothesis Dealing with the NCBI Taxonomy database SCRIPTS: orthoXML ETE’s Reference Guide ETE Toolkit Docs » The ETE tutorial View page source The ETE tutorial¶ Contents: Working With Tree Data Structures Trees Reading and Writing Newick Trees Reading newick trees Writing newick trees Understanding ETE Trees Basic tree attributes Root node on unrooted trees? Browsing trees (traversing) Getting Leaves, Descendants and Node’s Relatives Traversing (browsing) trees Advanced traversing (stopping criteria) Iterating instead of Getting Finding nodes by their attributes Checking the monophyly of attributes within a tree Caching tree content for faster lookup operations Node annotation Comparing Trees Calculate distances between trees Robinson-foulds distance Modifying Tree Topology Creating Trees from Scratch Deleting (eliminating) and Removing (detaching) nodes Pruning trees Concatenating trees Copying (duplicating) trees Solving multifurcations Tree Rooting Working with branch distances Getting distances between nodes getting midpoint outgroup The Programmable Tree Drawing Engine Overview Interactive visualization of trees Rendering trees as images Customizing the aspect of trees Tree style Node style Node faces layout functions Combining styles, faces and layouts Fixed node styles Node backgrounds Img Faces Bubble tree maps Trees within trees Phylogenetic trees and sequence domains Creating your custom interactive Item faces Phylogenetic Trees Overview Linking Phylogenetic Trees with Multiple Sequence Alignments Visualization of phylogenetic trees Adding taxonomic information Automatic control of species info Automatic (and custom) control of the species info Manual control of the species info Detecting evolutionary events Species Overlap (SO) algorithm Tree reconciliation algorithm A closer look to the evolutionary event object Relative dating phylogenetic nodes Implementation Automatic rooting (outgroup detection) Working with duplicated gene families Treeko (splitting gene trees into species trees) Splitting gene trees by duplication events Collapse species specific duplications Clustering Trees Overview Loading ClusterTrees Visualization of matrix associated Trees Cluster Validation Example Phylogenetic XML standards NeXML Reading NeXML projects NeXML tree manipulation and visualization PhyloXML Loading PhyloXML projects from files Creating PhyloXML projects from scratch Interactive web tree visualization NO X system available? Installing a X server Servers Desktops Configuring the web sever Implementation of WebTreeApplications Testing Evolutionary Hypothesis Extension Requirements: Overview The working directory Descriptive analysis Branch model Site model Hypothesis Testing Test on sites Test on branches Test on branch-sites Utilities Load precomputed evolutionary model References Dealing with the NCBI Taxonomy database Setting up a local copy of the NCBI taxonomy database Upgrading the local database Getting taxid information Getting descendant taxa Getting NCBI species tree topology Automatic tree annotation using NCBI taxonomy SCRIPTS: orthoXML OrthoXML parser The etree2orthoxml script Usage Example: Using custom evolutionary annotation Example: Automatic detection of species names Example: Tree rooting Next Previous © Copyright 2015, The ETE Toolkit Team. Last updated on Mar 18, 2016. Built with Sphinx using a theme provided by Read the Docs.